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Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach
A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be as...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339591/ https://www.ncbi.nlm.nih.gov/pubmed/22558535 http://dx.doi.org/10.1007/s13205-011-0006-8 |
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author | Singh, Abhishek A. Sivakumar, Dakshinamurthy Somvanshi, Pallavi |
author_facet | Singh, Abhishek A. Sivakumar, Dakshinamurthy Somvanshi, Pallavi |
author_sort | Singh, Abhishek A. |
collection | PubMed |
description | A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and CUPSAT servers predicted eleven nsSNPs to be intolerant, thirteen nsSNP to be damaging and two nsSNPs have the potential to destabilize protein structure. The nsSNP rs11666150 was predicted to be damaging by all three servers and its mutant structure showed significant increase in overall energy. FASTSNP predicted twenty SNPs to be present in splicing modifier binding sites while rSNP module from MAPPER server predicted nine SNPs to influence the binding of transcription factors. The results from the study may provide vital clues in establishing affect of polymorphism on phenotype and in elucidating drug response. |
format | Online Article Text |
id | pubmed-3339591 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-33395912012-05-01 Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach Singh, Abhishek A. Sivakumar, Dakshinamurthy Somvanshi, Pallavi 3 Biotech Original Article A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and CUPSAT servers predicted eleven nsSNPs to be intolerant, thirteen nsSNP to be damaging and two nsSNPs have the potential to destabilize protein structure. The nsSNP rs11666150 was predicted to be damaging by all three servers and its mutant structure showed significant increase in overall energy. FASTSNP predicted twenty SNPs to be present in splicing modifier binding sites while rSNP module from MAPPER server predicted nine SNPs to influence the binding of transcription factors. The results from the study may provide vital clues in establishing affect of polymorphism on phenotype and in elucidating drug response. Springer Berlin Heidelberg 2011-04-27 2011-07 /pmc/articles/PMC3339591/ /pubmed/22558535 http://dx.doi.org/10.1007/s13205-011-0006-8 Text en © The Author(s) 2011 https://creativecommons.org/licenses/by/4.0/ This article is published under license to BioMed Central Ltd. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited. |
spellingShingle | Original Article Singh, Abhishek A. Sivakumar, Dakshinamurthy Somvanshi, Pallavi Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title | Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title_full | Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title_fullStr | Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title_full_unstemmed | Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title_short | Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach |
title_sort | cataloguing functionally relevant polymorphisms in gene dna ligase i: a computational approach |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339591/ https://www.ncbi.nlm.nih.gov/pubmed/22558535 http://dx.doi.org/10.1007/s13205-011-0006-8 |
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